/**
 * @file src/DotBracket.h
 *
 * @date 14-may-2013
 *
 * @author Youri Hoogstrate
 * @author Lisa Yu
 *
 * @section LICENSE
 * yh-kt-fold can predict RNA 2D structures including K-turns.
 * Copyright (C) 2012-2013 Youri Hoogstrate
 *
 * This file is part of yh-kt-fold.
 *
 * yh-kt-fold is free software: you can redistribute it and/or modify
 * it under the terms of the GNU General Public License as published by
 * the Free Software Foundation, either version 3 of the License, or
 * (at your option) any later version.
 *
 * yh-kt-fold is distributed in the hope that it will be useful,
 * but WITHOUT ANY WARRANTY; without even the implied warranty of
 * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
 * GNU General Public License for more details.
 *
 * You should have received a copy of the GNU General Public License
 * along with this program. If not, see <http://www.gnu.org/licenses/>.
 */



#include "main.h"



/**
 * @brief Maintans a 2D structure in DotBracket format, and is maintained by the Zuker::traceback() function.
 *
 * @section DESCRIPTION
 * Maintains a DotBracket formatted 2D structure (without pseudo-knotting)
 */
class DotBracket
{
	public:
		// Initialize
		DotBracket();
		void initPairings();
		
		// DotBracket specific
		void store(int arg_i, int arg_j);
		int  find(int arg_i);
		void format(int arg_rnaSequenceLength);
		
	private:
		int basepairs[MAXLEN][2];
		int position;
};
